Couple things you guys could try..
for duo core cpus: while the game is running, go to the task manager and find Aquaria.exe in the processes list. Then right click and choose "Set Affinity..." and uncheck all but one of the CPU cores.
for everyone: edit usersettings.xml and change
<FpsSmoothing v="30" />
to
<FpsSmoothing v="0" />
Alternatively, try higher values (60, 90, 120)